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HERA: a web server for host element reference-based aligner
Leidy-Alejandra G Molano1,2, Pascal Hirsch1, Andreas Keller1,2,3
1Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany.
Nucleic Acids Research
|May 14, 2026
Summary
HERA is a web server for comparing bacterial plasmids and circular DNA. It offers intuitive visualization and analysis of sequence similarity and genetic elements, simplifying comparative genomics for researchers.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Plasmids are crucial for bacterial adaptation and antimicrobial resistance spread.
- Existing tools often lack plasmid-specific comparative analysis features.
- There is a need for accessible, web-based plasmid analysis platforms.
Purpose of the Study:
- To introduce HERA, a novel web server for plasmid visualization and comparison.
- To provide an intuitive platform for comparative genomics of circular DNA molecules.
- To facilitate the analysis of genetic elements and antimicrobial resistance dissemination.
Main Methods:
- Utilizes BLAST alignment against reference sequences for comparative analysis.
- Employs interactive circular genome visualization.
- Incorporates a plasmid-specific annotation pipeline for typing and detection.
Main Results:
- HERA simplifies exploring sequence similarity and conserved regions in plasmids.
- The tool identifies antimicrobial resistance genes, mobile elements, and replicon types.
- Automatic selection of the most appropriate reference sequence is provided.
Conclusions:
- HERA offers an accessible, web-based solution for plasmid comparative genomics.
- The platform aids in understanding bacterial adaptation and antimicrobial resistance.
- HERA supports researchers without requiring local computational infrastructure.
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